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For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity‐rich regions (HRR) in a subpopulation of Guzerá dual‐purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5), and by the proportion of homozygous loci (FHOM) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate‐high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree‐based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied. [ABSTRACT FROM AUTHOR]

We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines ( SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions. [ABSTRACT FROM AUTHOR]

Pig breeding companies keep relatively small populations of pure sire and dam lines that are selected to improve the performance of crossbred animals. This design of the pig breeding industry presents challenges to the implementation of genomic selection, which requires large data sets to obtain highly accurate genomic breeding values. The objective of this study was to evaluate the impact of different reference sets (across population and multipopulation) on the accuracy of genomic breeding values in 3 purebred pig populations and to assess the potential of using crossbreed performance in genomic prediction. Data consisted of phenotypes and genotypes on animals from 3 purebred populations (sire line [SL] 1, n = 1,146; SL2, n = 682; and SL3, n = 1,264) and 3 crossbred pig populations (Terminal cross [TER] 1, n = 183; TER2, n = 106; and TER3, n = 177). Animals were genotyped using the Illumina Porcine SNP60 Beadchip. For each purebred population, within-, across-, and multipopulation predictions were considered. In addition, data from the paternal purebred populations were used as a reference set to predict the performance of crossbred animals. Backfat thickness phenotypes were precorrected for fixed effects and subsequently included in the genomic BLUP model. A genomic relationship matrix that accounted for the differences in allele frequencies between lines was implemented. Accuracies of genomic EBV obtained within the 3 different sire lines varied considerably. For within-population prediction, SL1 showed higher values (0.80) than SL2 (0.61) and SL3 (0.67). Multipopulation predictions had accuracies similar to within-population accuracies for the validation in SL1. For SL2 and SL3, the accuracies of multipopulation prediction were similar to the within-population prediction when the reference set was composed by 900 animals (600 of the target line plus 300 of another line). For across-population predictions, the accuracy was mostly close to zero. The accuracies of predicting crossbreed performance were similar for the 3 different crossbred populations (ranging from 0.25 to 0.29). In summary, the differences in accuracy of the within-population scenarios may be due to line divergences in heritability and genetic architecture of the trait. Within- and multipopulation predictions yield similar accuracies. Across-population prediction accuracy was negligible. The moderate accuracy of prediction of crossbreed performance appears to be a result of the relationship between the crossbreed and its parental lines. [ABSTRACT FROM AUTHOR]

The local Brazilian pig breed Piau is a lard-type pig that has undergone a breeding and selection process devised by the veterinarian Antonio Teixeira Vianna in 1939. The objective of the program was to develop a dual purpose animal, that is an animal suitable for the production of both fat and meat. The main characteristics of the Piau breed are rusticity, adaptability and high disease resistance. The conservation status of the breed is threatened, and in 1998, the Pig Breeding Farm at Universidade Federal de Viçosa (UFV, Viçosa, MG, Brazil) started a Piau herd for the purposes of conservation and use in genetic studies. The objectives of the present study were to describe the Piau genetic conservation program of the Universidade Federal de Viçosa (UFV) and to evaluate a range of population parameters to generate information for monitoring and improving the program. Population genetic structure analysis was performed using a pedigree file of 1349 animals and ENDOG v 4.8 software. The Piau conservation program has data and a collection of pedigree registers going back to the introduction of the first animals to the Pig Breeding Farm. The program used mating control, which is based on the mating of animals with the lowest pedigreebased relationships and on the maintenance of all the population’s founding families. The effective numbers of founders and ancestors in the studied Piau population are 9 and 8 animals, respectively. The average inbreeding coefficient (F), the average relatedness coefficient (AR) and the effective population size are 6.55 %, 19.74 % and 18.59, respectively. The findings support an increase in the effective population size of this population through the introduction of animals from other populations, as the small number of founders makes inbreeding control difficult. [ABSTRACT FROM AUTHOR]

The article discusses linkage disequilibrium (LD) which determines the number of single nucleotide polymorphism (SNP) which can be used for association and genomic studies in a genome. It states that LD also influences the genomic breeding values accuracy. The studies involved the marker reduction by selecting SNP which can be used for haplotype block used in association mapping. The differences in haplotype block can be used for future studies of differences across the animal cell lines.

Seventy-two pigs of three genetic groups (Brazilian indigenous breed Piau, Commercial line and Crossbred) of both sexes were slaughtered at four live weights (30, 60, 90 and 120 kg). Intramuscular fat (IMF) content in Longissimus dorsi muscle of each animal was extracted and correlated with candidate gene mRNA expression ( ATN1, EEF1A2, FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1). Within slaughter weight of 120 kg, Piau and Crossbred pigs showed higher IMF content (p < 0.05) than commercial animals, with 2.48, 2.08 and 1.00% respectively. Barrows presented higher values of IMF (p < 0.05) than gilts (1.54 and 1.30% respectively). Gene expression of EEF1A2, FABP3, LDLR, OBSCN, PDHB, TRDN and RYR1 were correlated with IMF (p < 0.05) using the whole dataset. For Piau data only, expression of FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1 showed correlation with IMF (p < 0.05). Genes that have important roles in lipid transportation inside the cell ( FABP3) and tissues ( LDLR) showed correlation with IMF of, respectively, 0.68 and 0.63 using the whole data set, and 0.90 and 0.91 using data from Piau animals. The highly positive correlation of the LDLR and FAPB3 expression with IMF content may confirm that these genes are important for fat deposition in the porcine L. dorsi muscle. [ABSTRACT FROM AUTHOR]

We aimed to estimate genetic parameters for the non-linear Gompertz growth curve parameters based on the two-step method and simulated data of a pig population. Data of true breeding values, growth curve parameters (a, b and k) and body weights at 1, 90, 210, 360 and 540 days of age were simulated for 1700 individuals. Afterwards, in the first stage of the two-step method, the Gompertz curves were fitted for each animal and the growth curve parameters were estimated. In the second step, considering the estimated parameters as phenotypes, animals' breeding values were predicted by multitrait analyses. The simulation and two-step processes were replicated 10 times. For each replicate, the genetic parameters, accuracies and biases were calculated. Moderate to high average heritabilities for the curve parameters [0.62 (0.04), 0.56 (0.04) and 0.57 (0.04) for a, b and k, respectively] show the possibility of effective selection of animals based on these parameters. High and favorable average genetic correlations, especially between the most important growth curve parameters [a and k, 0.93 (0.01)], shows that selection for increased mature weight (a) will also increase maturation rate (k). High average accuracies [0.84 (0.02), 0.82 (0.02) and 0.83 (0.02)] and low average biases [0.06 (0.06), 0.06 (0.06) and 0.07 (0.07) for a, b, and k, respectively] indicate that the two-step approach is feasible for predicting breeding values for growth curve parameters and for dealing with longitudinal body weight measurements. [ABSTRACT FROM AUTHOR]

In the current study we have performed two experiments to evaluate the effects of adipogenic induction media on dedifferentiated fat (DFAT) cells redifferentiation into mature adipocytes. In experiment 1, we aimed to evaluate whether it is necessary to use insulin in the induction media to allow DFAT cells differentiation into mature adipocytes by establishing two experimental treatments where insulin was either withdrawn from the culture medium, after 72 h of a normal induction period (Treatment 1: Insulin - ) or kept in culture media (Treatment 2: Insulin + ) for 16 d. In experiment 2, we aimed to evaluate if the lack of 3-isobutyl-1-methylxanthine (IBMX) in the induction medium would affect the differentiation of DFAT cells into mature adipocytes. For that, DFAT cells were induced to differentiate into lipid assimilating adipocytes using an induction medium containing IBMX (Treatment 1: IBMX + ) or without IBMX (Treatment 2: IBMX - ) during the first 72 h of induction. In both experiments we have evaluated the mRNA expression of lipid metabolism markers and cell morphology through Oil-Red staining as indicators of differentiation of DFAT cells into lipid-assimilating cells. The results of Experiment 1 revealed no differences in mRNA expression for any of the lipid metabolism markers with exception of GLUT4 ( P =0.02), which was greater in Insulin - compared to Insulin + treatment. Similarly, no differences were observed for mRNA expression of adipogenic markers between IBMX + and IBMX - treatments with exception of FABP4 ( P =0.01), which was greater for the IBMX - compared to IBMX + treatment. In both experiments we did not observed any differences in cell morphology among treatments. Our results suggest that neither insulin nor IBMX are required to accelerate redifferentiation process of pig-derived DFAT cells. [ABSTRACT FROM AUTHOR]

1. Uniformity in animal products is an important aspect of the production system. Several studies have reported estimates of genetics on residual variance in different species, indicating that it could be exploited to improve uniformity by selection. Nevertheless, there are no reports about the possibilities of such a selection strategy in meat quail. 2. Records of hatching weight (HW) and body weight at 42 days (W42) of female and male birds from two meat quail lines (UFV1 and UFV2) were analysed. A three-step genetic evaluation was used to investigate the effect of genetic variation on residual variance of HW and W42 in both lines. In Step 1, a single-trait model was fitted to the data. In Step 2, log-transformed squared estimated residuals (ln(ê2)) were evaluated for these traits. In Step 3, a multi-trait analysis was performed to estimate the genetic correlation between the additive genetic effects for HW, W42, and their respective ln(ê2). 3. The heritability estimates ranged from 0.12 to 0.23 for HW and from 0.22 to 0.35 for W42. The estimated heritabilities for the residual part were low and ranged from 0.0003 to 0.02 for both traits, and the genetic coefficient of variation residual variance estimates ranged from 0.31 to 0.42 for HW and from 0.09 to 0.25 for W42. Genetic correlations between the means (HW and W42) and ln(ê2) values were both positive and did not differ from zero, indicating no association between mean and ln(ê2). 4. In conclusion, the uniformity of HW and W42 could be improved by selecting for lower residual variance in both meat quail lines, but the accuracy of selection may be low due to low heritability for uniformity, mainly for W42. [ABSTRACT FROM AUTHOR]

1. The aim of this study was to investigate the associations between several carcass, performance and meat quality traits in broilers through factor analysis and use the latent variables (i.e. factors) as pseudo-phenotypes in genetic evaluations. 2. Factors were extracted using the principal components method and varimax rotation algorithm. Genetic parameters were estimated via Bayesian inference under a multiple-trait animal model. 3. All factors taken together explained 71% of the original variance of the data. The first factor, denominated as 'weight', was associated with carcass and body weight traits; and the second factor, defined as 'tenderness', represented traits related to water-holding capacity and shear force. The third factor, 'colour', was associated with traits related to meat colour, whereas the fourth, referenced as 'viscera', was related to heart, liver and abdominal fat. 4. The four biological factors presented moderate to high heritability (ranging from 0.35 to 0.75), which may confer genetic gains in this population. 5. In conclusion, it seems possible to reduce the number of traits in the genetic evaluation of broilers using latent variables derived from factor analysis. [ABSTRACT FROM AUTHOR]

Summary: Genome‐wide association studies (GWASes) have been performed to search for genomic regions associated with residual feed intake (RFI); however inconsistent results have been obtained. A meta‐analysis may improve these results by decreasing the false‐positive rate. Additionally, pathway analysis is a powerful tool that complements GWASes, as it enables identification of gene sets involved in the same pathway that explain the studied phenotype. Because there are no reports on GWAS pathways‐based meta‐analyses for RFI in beef cattle, we used several GWAS results to search for significant pathways that may explain the genetic mechanism underlying this trait. We used an efficient permutation hypothesis test that takes into account the linkage disequilibrium patterns between SNPs and the functional feasibility of the identified genes over the whole genome. One significant pathway (valine, leucine and isoleucine degradation) related to RFI was found. The three genes in this pathway—methylcrotonoyl‐CoA carboxylase 1 (MCCC1), aldehyde oxidase 1 (AOX1) and propionyl‐CoA carboxylase alpha subunit (PCCA)—were found in three different studies. This same pathway was also reported in a transcriptome analysis from two cattle populations divergently selected for high and low RFI. We conclude that a GWAS pathway‐based meta‐analysis can be an appropriate method to uncover biological insights into RFI by combining useful information from different studies. [ABSTRACT FROM AUTHOR]

Genomic selection is applied to dairy cattle breeding to improve the genetic progress of purebred (PB) animals, whereas in pigs and poultry the target is a crossbred (CB) animal for which a different strategy appears to be needed. The source of information used to estimate the breeding values, i.e., using phenotypes of CB or PB animals, may affect the accuracy of prediction. The objective of our study was to assess the direct genomic value (DGV) accuracy of CB and PB pigs using different sources of phenotypic information. Data used were from 3 populations: 2,078 Dutch Landrace-based, 2,301 Large White-based, and 497 crossbreds from an F1 cross between the 2 lines. Two female reproduction traits were analyzed: gestation length (GLE) and total number of piglets born (TNB). Phenotypes used in the analyses originated from offspring of genotyped individuals. Phenotypes collected on CB and PB animals were analyzed as separate traits using a single-trait model. Breeding values were estimated separately for each trait in a pedigree BLUP analysis and subsequently deregressed. Deregressed EBV for each trait originating from different sources (CB or PB offspring) were used to study the accuracy of genomic prediction. Accuracy of prediction was computed as the correlation between DGV and the DEBV of the validation population. Accuracy of prediction within PB populations ranged from 0.43 to 0.62 across GLE and TNB. Accuracies to predict genetic merit of CB animals with one PB population in the training set ranged from 0.12 to 0.28, with the exception of using the CB offspring phenotype of the Dutch Landrace that resulted in an accuracy estimate around 0 for both traits. Accuracies to predict genetic merit of CB animals with both parental PB populations in the training set ranged from 0.17 to 0.30. We conclude that prediction within population and trait had good predictive ability regardless of the trait being the PB or CB performance, whereas using PB population(s) to predict genetic merit of CB animals had zero to moderate predictive ability. We observed that the DGV accuracy of CB animals when training on PB data was greater than or equal to training on CB data. However, when results are corrected for the different levels of reliabilities in the PB and CB training data, we showed that training on CB data does outperform PB data for the prediction of CB genetic merit, indicating that more CB animals should be phenotyped to increase the reliability and, consequently, accuracy of DGV for CB genetic merit. [ABSTRACT FROM AUTHOR]

We aimed to investigate the impacts of ruminal undegradable protein (RUP) enriched diet during late gestation on performance of pregnant beef cows and skeletal muscle growth of the offspring. From 180d of gestation to parturition, a total of 31 Brahman pregnant cows were randomly assigned to one of the experimental treatments: High-RUP diet (H-RUP, n = 17), and control diet (CTRL, n = 14). Maternal results showed no differences (P > 0.05) in dry matter intake, and total digestible nutrients intake between treatments. However, crude protein intake and the RUP intake were greater (P < 0.01) in H-RUP, while CTRL group had greater (P < 0.01) rumen degradable protein intake. Cows from H-RUP group were heavier (P < 0.01) at parturition and had greater (P = 0.01) average daily gain. Blood levels of nitric oxide tended (P = 0.06) to be greater in H-RUP, while blood glucose levels were not altered (P > 0.60) by RUP-enriched diet. Blood aminoacidic profile showed greater (P = 0.02) concentrations of methionine in CTRL group, and greater (P < 0.01) concentrations of the branched chain amino acids in H-RUP cows. A greater (P = 0.04) number of muscle fibers were observed in the H-RUP offspring, while a tendency (P = 0.07) of greater muscle fiber diameter was observed in CTRL offspring. Gene expression analysis indicated higher (P < 0.01) expression of the satellite cells marker (PAX7) in CTRL offspring. In contrast, the expression of the markers of fibro-adipogenic progenitor cells (PDGFRα), and adipogenesis (ZFP423, PPARγ, C/EBPα) were higher in the skeletal muscle of H-RUP offspring. Consistently , at the protein level the greater abundance of ZFP423 (P = 0.03), and PPARγ (P = 0.01) were observed in H-RUP offspring. Moreover, the expression of the fibrogenic marker (TGFβ) was higher (P = 0.01) in H-RUP offspring. Our findings suggest that supplementing pregnant beef cows during late gestation may increase the availability of amino acids, responsible to maintain maternal body conditions and to change the skeletal muscle characteristics of the offspring. Since the resulting offspring from H-RUP treatment showed greater number of muscle fiber and an increase in the process of intramuscular adipogenesis our data suggest that a RUP-enriched diet for pregnant cows at late gestation may be beneficial for the achievement of better carcasses at slaughter. However, the feeding strategy showed no changes in the offspring's performance during the growing phase. • Ruminal undegradable protein (RUP) supplementation during late gestation improved maternal body conditions at parturition. • The blood levels of nitric oxide tended to be greater in cows supplemented with RUP. • Greater number of muscle fibers in the offspring resulting from maternal RUP supplementation. • RUP supplementation during late gestation improved offspring's adipogenesis. [ABSTRACT FROM AUTHOR]